Why would you want one league for the whole school? There are too many sports for that to work.
Outside of CH and McD, pretty much every other MIAA school would have major issues with this. CH has the huge enrollment to boost its success and MCD has the recruiting angle. All other schools flow pretty freely, depending on the sport and year.
I think allowing programs to move every 2 years is good for parity. If a school knows they have a strong or weak class coming, they can move accordingly. I think that's a good thing.